It may not have been what U.S. Secretary of State Hillary Clinton was expecting on her first visit to Cairo since Egyptians voted in their first democratic presidential election in the country’s history last month. But for a portion of her two-day visit to the Arab world’s largest country, Clinton found herself confronting the ultimate reversal of Arab-world conspiracy theories. According to some of the civil-society leaders and activists she met with — as well as some who refused to meet with her at all — the U.S., once allegedly the backer of Hosni Mubarak’s authoritarian regime, is now a supporter of the Islamist Muslim Brotherhood. One Egyptian-American Christian who attended a meeting with the Secretary of State on Sunday even cited Republican Congresswoman Michele Bachman’s recent assertion that the Obama Administration is pursuing a closeted pro-Muslim agenda.

“They had their concerns and were even angry with the situation on the part of the American Administration, which has implied in the past few weeks that it is blessing the rise of political Islam in Egypt,” explained Youssef Sidhom, a prominent Christian activist and newspaper editor, who was present at Clinton’s Sunday meeting with Egyptian-Christian leaders. Egypt’s Christian minority, and indeed many secularists, have grown increasingly vocal about their fears of an Islamist rise since the election of Muslim Brotherhood candidate Mohamed Morsy as President in June. Sidhom said that Clinton convincingly reassured the meeting on Sunday that the U.S. has not and will not side with any political party.

But the confrontation underscores the increasingly murky political waters that the U.S. Administration has sought to navigate in the 18 months since a popular uprising ended the 30-year reign of longtime U.S. ally Mubarak. Last month’s presidential vote propelled Morsy, an official from the once banned Muslim Brotherhood, into the country’s highest seat of power. And the power struggle that has since ensued between Morsy and the unelected military generals, who took power when Mubarak stepped down and have proven unwilling to fully let go, has only deepened the political swamp.

One U.S. official confided to TIME on Sunday that the Secretary of State’s first postelectoral visit was challenging in large part due to the lack of obvious counterparts for Clinton and her staff to meet with amid the ongoing power struggle, since Morsy has yet to appoint a Cabinet. Another official said that within the status quo, it’s also sometimes unclear — even among military leaders and within the presidency — which individuals are the real decisionmakers.

Egyptians have long propagated conspiracy theories to explain the generally opaque doings of their corrupt government. And their suspicions of the U.S. have only grown in the past 18 months, as U.S. officials have sought to promote democracy in the country, while simultaneously seeking guarantees from the unelected junta of respect for U.S. interests, particularly Egypt’s peace treaty with Israel. U.S.-Egyptian tensions hit a new high in January when Egypt’s prosecution of several prominent American NGOs had Washington threatening to halt Egypt’s $1.3 billion in annual military aid. But the retrospective emptiness of those threats — despite the lack of a resolution to the NGO crisis, and recent moves by the military to consolidate rather than cede power — may have only bolstered the generals’ confidence, and hammered in another uncomfortable truth for U.S. officials: American influence in Egypt is waning.

Perhaps in acknowledgment of that fact, Clinton struck a decidedly softer tone on the military during her visit, compared with the statements made by the State Department last month after the generals dissolved the country’s elected parliament and seized legislative control for themselves. After meeting with President Morsy on Saturday, Clinton told reporters that the U.S. continues to support Egypt’s “full transition to civilian rule with all that entails,” and she outlined a $1 billion debt-relief package. But she trod cautiously around the military’s recent power grab, saying: “The issues around the parliament, the constitution have to be resolved between and among Egyptians.”

Human-rights groups say that the military council has sent more than 10,000 civilians to closed military tribunals in the past 18 months, and it has been repeatedly implicated in the use of violence and torture against protesters. Activists warn that those abuses may continue as long as the military maintains a role in Egyptian politics. But it’s not clear whether Clinton broached these issues when she met with Field Marshal Mohamed Hussein Tantawi, the head of the Supreme Council of the Armed Forces (SCAF), on Sunday. A high-ranking State Department official only said that the two had discussed Egypt’s transition, Tantawi’s “ongoing dialogue with President Morsy,” minority rights and the Obama Administration’s proposed economic-aid package.

In her remarks on Saturday, Clinton commended the SCAF “for representing the Egyptian people in the revolution, as compared to what we’re seeing in Syria, which is the military murdering their own people.” The comparison drew frustrated responses from some activists. “Kind of a low bar,” tweeted one anonymous Cairene. “‘Thanks for not butchering children!’ Maybe SCAF will reply with ‘Thanks for not invading us!'” But as Clinton departed for Israel on Sunday afternoon for the final leg of a world tour that included Afghanistan and East Asia, U.S. officials also seemed to suggest that their hands were tied when it comes to exerting much influence in Egypt’s unfolding political drama. “Only Egyptians can choose their leaders,” is the message that Clinton sought to convey in all of her meetings, stressed one senior State Department official. “We have not supported any candidate, any party, and we will not. But what we do support is a full transition to democratic civilian governance.”